Make settings variables for saving intermediate files more intuitive

[bitterbark]

To try to save intermediate netcdf files, I set all the save flags to true:
// Set flag to have PODs save postscript figures in addition to bitmaps.
"save_ps": true,
// Set flag to have PODs save netCDF files of processed data.
"save_nc": true,
// Set flag to save all processed data except netcdf files.
"save_non_nc": true,

Unfortunately, the effect of save_non_nc = true is that save_nc is ignored (and therefore the nc files are deleted).
In the code this is even commented as counter-intuitive # delete all generated data (flag is a misnomer)

I propose we make it clear to users what they are saving.

Also, I'm not sure what these 'non_nc' files are expected to be, considering we are strongly encouraging (and reviewing code) to enforce writing nc files, right?

Or easier IMHO would be to have an overrriding save_all flag and scrap 'save_non_nc':
if not save_all:
if not save_ps:
delete ps files
if not save_nc:
delete nc files

If we need to keep the "non_nc" files, let's call this save_other, and the code can be:
if not save_all:
if not save_ps:
delete ps files
if not save_nc:
delete nc files
if not save_other:
delete all but nc & ps files

I can fold this into my next pull request if there is agreement, and of course I'm open to suggestions of better ways if anyone posts them.